BN1305 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 3.7795e-04 7.2502e-03
Layer 1 6.9443e-04 4.6006e-02
Layer 5 1.7370e-03 4.7071e-03
Layer 2 2.0412e-03 8.7501e-02
Layer 3 2.0847e-03 4.7338e-02
Layer 6 3.2765e-03 6.0904e-03

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.3867 0.6410
SH3GL2 Layer 5 2.2363 0.5024
ATP6V1B2 Layer 6 2.0117 0.4967
TUBB2A Layer 5 2.2422 0.4915
YWHAG Layer 5 2.0391 0.4842
G3BP2 Layer 6 1.9678 0.4788
SYN2 Layer 5 2.2871 0.4768
SYP Layer 5 2.2129 0.4762
STX1A Layer 5 1.9404 0.4758
ATP5F1A Layer 5 2.0586 0.4671
DNAJC6 Layer 5 2.0859 0.4628
APBB1 Layer 5 2.0547 0.4593
ATP1A3 Layer 5 2.0586 0.4557
NAPB Layer 5 2.0684 0.4518
NDRG4 Layer 5 2.0918 0.4512
DCLK1 Layer 6 2.2930 0.4500
ENO2 Layer 5 2.1348 0.4492
EIF4A2 Layer 5 2.1777 0.4486
STMN1 Layer 5 2.0352 0.4462
DIRAS2 Layer 6 2.5840 0.4453
HINT1 Layer 5 2.1797 0.4450
SYT1 Layer 5 2.0488 0.4446
NRN1 Layer 5 2.3398 0.4440
EFHD2 Layer 5 2.0918 0.4438
FXYD6 Layer 5 2.1719 0.4424
CPLX1 Layer 4 2.1250 0.4414
TAGLN3 Layer 6 2.2930 0.4410
ATP6V1A Layer 6 2.2930 0.4354
TUBA4A Layer 5 2.0215 0.4343
NAP1L2 Layer 6 2.0215 0.4305
MTCH1 Layer 5 2.1191 0.4299
ATP6V0B Layer 5 2.1348 0.4297
MDH1 Layer 5 2.1816 0.4291
KIF3C Layer 6 2.0283 0.4274
HSPA8 Layer 5 2.1484 0.4273
SERPINI1 Layer 5 2.2324 0.4272
B4GAT1 Layer 5 2.0488 0.4267
CDC42SE2 Layer 5 1.9629 0.4259
CLSTN2 Layer 5 2.4609 0.4256
CHCHD10 Layer 5 1.9014 0.4251
NUDT4 Layer 5 2.0352 0.4249
PAFAH1B1 Layer 5 2.0723 0.4245
TUBB3 Layer 5 2.1680 0.4239
RAB6B Layer 6 2.0781 0.4236
PGAM1 Layer 5 2.0889 0.4235
SOD1 Layer 5 1.9854 0.4231
GRINA Layer 5 2.0254 0.4230
PINK1 Layer 5 2.0254 0.4225
PFKP Layer 5 2.2100 0.4222
CHGA Layer 5 1.9990 0.4220

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1305
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1305_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1305/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1305/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1305/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1305/report/PD/BN1305_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1305/report/PD/BN1305_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:08:47
  • Number of Processes: 10
  • Spending Time: 0h 3m